7BVH

Crystal structure of arabinosyltransferase EmbC2-AcpM2 complex from Mycobacterium smegmatis complexed with di-arabinose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history



Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Integral membrane indolylacetylinositol arabinosyltransferase EmbC
A, B
1,113Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: embCMSMEI_6219
EC: 2.4.2.34
Membrane Entity: Yes 
UniProt
Find proteins for A0R612 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R612 
Go to UniProtKB:  A0R612
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R612
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Meromycolate extension acyl carrier protein
C, D
99Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0R0B3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R0B3 
Go to UniProtKB:  A0R0B3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R0B3
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose
E, J
2N/A
Glycosylation Resources
GlyTouCan:  G34232WB
GlyCosmos:  G34232WB
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose
F, G, H, I, K
F, G, H, I, K, L
2N/A
Glycosylation Resources
GlyTouCan:  G66120GK
GlyCosmos:  G66120GK
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BXY
Query on BXY

Download Ideal Coordinates CCD File 
O [auth A],
P [auth A],
S [auth B],
T [auth B]
alpha-D-arabinofuranose
C5 H10 O5
HMFHBZSHGGEWLO-MBMOQRBOSA-N
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
N [auth A],
R [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CA
Query on CA

Download Ideal Coordinates CCD File 
M [auth A],
Q [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.08α = 90
b = 176.33β = 90
c = 207.77γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2017YFC0840300
National Science Foundation (NSF, China)China81520108019
Chinese Academy of SciencesChinaXDB29020000
Medical Research Council (MRC, United Kingdom)United KingdomMR/S000542/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-05-13
    Changes: Database references
  • Version 1.2: 2020-07-01
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary